Tuesday 21 February 2012 11.20 EST
First published on Tuesday 21 February 2012 11.20 EST

Nato forces have rushed to apologise for discarding and possibly burning copies of the Qur'an, as thousands of furious Afghans gathered to protest outside Bagram military airbase.

Some carried ancient hunting rifles and others used slingshots to pelt the outer walls of the airbase with stones for several hours, despite the bitter cold, shouting "down with America" and other slogans.

The crowd swelled to up to 3,000, and police stationed on roads leading to the base turned back other would-be protesters from further away, according to General Muhammad Akram Bekzad, Parwan province's police chief. At least 12 civilians were injured by rubber bullets fired by coalition soldiersto control the protesters, said Haji Abdul Aziz, police chief for Bagram district. Nato-led forces confirmed that "some non-lethal munitions were used to help disperse the crowd."

Any destruction of, or damage to, Islam's holy book is a highly sensitive issue in Afghanistan that has sparked sometimes deadly riots in the past. As details of the apparent burning emerged, the top US and Nato general in Afghanistan apologised and promised an inquiry – seemingly to try to contain the spreading outrage.

"I assure you … I promise you … this was NOT intentional in any way," General John Allen said in a statement addressed to the "noble people of Afghanistan".

Copies of the Qur'an taken from prisoners at the airbase had been handed over for incineration late on Monday, and were spotted by Afghan workers, according to Afghan and western officials.

It is routine practice to burn waste documents on military bases in Afghanistan, and Bekzad said the Qur'ans were discarded with many other papers.

A spokesman for coalition forces, Lieutenant Colonel Jimmie Cummings, said the books were sent for incineration by mistake, but declined to comment further pending the investigation. "The decision to burn had nothing to do with the material being religious in nature or related to Islam … it was an error."

He said coalition forces were not yet sure how much religious material had been sent for incineration and whether any Qur'ans had been burned before the Afghan workers intervened. Haji Ahmad Zaki Zahed, head of the Parwan provincial council, said 17 copies were rescuedbefore the flames took hold. "I talked with five representatives of the workers, who showed me the pieces of the holy book, which I saw for myself were partly burned," he said.

In a further sign of Nato concern over the incident, Allen said all 130,000 foreign troops serving in Afghanistan would be trained within the next two weeks on how to identify, store and handle religious material.

When the US cleric Terry Jones burned a copy of the Qur'an last year it triggered deadly protests across Afghanistan. Nine people were killed and more than 80 injured in a riot in southern Kandahar city, and in normally peaceful northern Mazar-i-Sharif, an angry crowd overran a United Nations compound and killed seven foreign employees, slitting the throat of one.

In response to the latest incident, protesters said they wanted to meet President Karzai on Tuesday evening or they would return to the gates of Bagram on Wednesday .

"I will decide whether to go back to my job when I get the results of the investigation," said Rahmatullah Nazari, a 27-year-old protester who has worked at Bagram airbase for nine years. He said troops had tried to burn a vehicle with more than 1,000 copies of the Qur'an inside, although both western and Afghan officials said the number was much lower. The figure was a reminder that rumours about desecration can also spread as fast as anger.

Nazari said he joined about 200 other protesters when he turned up at 3am for his shift, and found the gates of the base locked. By 6am or 7am, the number at had swelled to more than 1,000. "The people were very emotional, tempers were high. Why did the Americans do this?"